[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

[Justin A. Lemkul]

Ye Yang wrote:
> Hi, everyone:
>       I am a new user of Gromacs, and I am running through the tutorial. 
> When I am trying to run the ligand-receptor binding tutorial from
>       
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
>      I met some trouble in adding ion.
>      Each time when I use genion, it shows:
> 
> Will try to add 0 NA ions and 6 CL ions.
> Select a continuous group of solvent molecules
> Group     0 (         System) has 33046 elements
> Group     1 (        Protein) has  1693 elements
> Group     2 (      Protein-H) has  1301 elements
> Group     3 (        C-alpha) has   163 elements
> Group     4 (       Backbone) has   489 elements
> Group     5 (      MainChain) has   653 elements
> Group     6 (   MainChain+Cb) has   805 elements
> Group     7 (    MainChain+H) has   815 elements
> Group     8 (      SideChain) has   878 elements
> Group     9 (    SideChain-H) has   648 elements
> Group    10 (    Prot-Masses) has  1693 elements
> Group    11 (    non-Protein) has 31353 elements
> Group    12 (          Other) has    15 elements
> Group    13 (            JZ4) has    15 elements
> Group    14 (          Water) has 31338 elements
> Group    15 (            SOL) has 31338 elements
> Group    16 (      non-Water) has  1708 elements
> Select a group: 15
> Selected 15: 'SOL'
> Number of (3-atomic) solvent molecules: 10446
> 
> Processing topology
> 
> Back Off! I just backed up temp.top to ./#temp.top.3#
> 
> -------------------------------------------------------
> Program genion_d, VERSION 4.5.4
> Source code file: gmx_genion.c, line: 285
> 
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of file 
> 'topol.top'
> 

Something doesn't match up here - the command backs up temp.top, but then 
complains it can't find SOL in topol.top.  Either genion is looking at the wrong 
file or your command is somehow wrong.

> I checked my topology file and it looks fine:
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
> 
> ; Include ligand topoloty
> #include "drg.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> 
> Protein
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> JZ4                 1     
> SOL             10446
> 
> One thing that might happen is in the genion source file,  I read 
> through it, and the problem either happens in loading the line to buf2, 
> or in the gmx_strcmp(buf2,"SOL"), since clearly the SOL_line is -1 
> aftermath.
> 
> The other thing I tried is to remove the ligand JZ4 part in both 
> topology and coordinates file, and in this case, it works perfectly for 
> adding ion. But in this way, I do not know how to insert my ligand into 
> the system since it might collide with solvent.
> 

If removal of the JZ4 line relieves the problem, perhaps there's a problem with 
that line, i.e. the line ending?  What type of system are you using?  Sometimes 
Windows line endings cause problems.  Always use a plain text editor and use 
dos2unix to process text files if you're on Windows.

Otherwise, the work-around is to not have genion work on the topology.  Make the 
corrections yourself.  Simple addition of ions and subtraction of water 
molecules is trivial.

-Justin

> Can someone help me with this problem?
> 
> Thank you all very much.
> 
> Ye Yang
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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